vital_status_tt: Determine vital status at end of follow-up depending on...

In marianschmidt/msSPChelpR: Helper Functions for Second Primary Cancer Analyses

Determine vital status at end of follow-up depending on pat_status - tidytable version

Description

Determine vital status at end of follow-up depending on pat_status - tidytable version

Usage

vital_status_tt(
  wide_df,
  status_var = "p_status",
  life_var_new = "p_alive",
  check = TRUE,
  as_labelled_factor = FALSE
)

Arguments

wide_df	dataframe or data.table in wide format
status_var	Name of the patient status variable that was previously created. Default is p_status.
life_var_new	Name of the newly calculated variable for patient vital status. Default is p_alive.
check	Check newly calculated variable life_var_new by printing frequency table. Default is TRUE.
as_labelled_factor	If true, output life_var_new as labelled factor variable. Default is FALSE.

Value

wide_df

Examples

#load sample data
data("us_second_cancer")

#prep step - make wide data as this is the required format
usdata_wide <- us_second_cancer %>%
                    msSPChelpR::reshape_wide_tidyr(case_id_var = "fake_id", 
                    time_id_var = "SEQ_NUM", timevar_max = 10)
                    
#prep step - calculate p_spc variable
usdata_wide <- usdata_wide %>%
                 dplyr::mutate(p_spc = dplyr::case_when(is.na(t_site_icd.2)   ~ "No SPC",
                                                       !is.na(t_site_icd.2)   ~ "SPC developed",
                                                       TRUE ~ NA_character_)) %>%
                 dplyr::mutate(count_spc = dplyr::case_when(is.na(t_site_icd.2)   ~ 1,
                                                              TRUE ~ 0))
                                                              
#prep step - create patient status variable
usdata_wide <- usdata_wide %>%
                  msSPChelpR::pat_status(., fu_end = "2017-12-31", dattype = "seer",
                                         status_var = "p_status", life_var = "p_alive.1",
                                         birthdat_var = "datebirth.1", lifedat_var = "datedeath.1")
 
#now we can run the function
msSPChelpR::vital_status_tt(usdata_wide, 
                        status_var = "p_status",
                        life_var_new = "p_alive_new", 
                        check = TRUE, 
                        as_labelled_factor = FALSE)

marianschmidt/msSPChelpR documentation built on Feb. 1, 2024, 6:45 a.m.